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<FONT color="green">001</FONT>    package edu.hawaii.myisern.model;<a name="line.1"></a>
<FONT color="green">002</FONT>    <a name="line.2"></a>
<FONT color="green">003</FONT>    import java.io.File;<a name="line.3"></a>
<FONT color="green">004</FONT>    import java.io.FileInputStream;<a name="line.4"></a>
<FONT color="green">005</FONT>    import java.io.FileOutputStream;<a name="line.5"></a>
<FONT color="green">006</FONT>    import java.io.OutputStream;<a name="line.6"></a>
<FONT color="green">007</FONT>    import java.nio.channels.FileChannel;<a name="line.7"></a>
<FONT color="green">008</FONT>    import java.util.ArrayList;<a name="line.8"></a>
<FONT color="green">009</FONT>    import java.util.Collections;<a name="line.9"></a>
<FONT color="green">010</FONT>    import java.util.HashMap;<a name="line.10"></a>
<FONT color="green">011</FONT>    import java.util.List;<a name="line.11"></a>
<FONT color="green">012</FONT>    import java.util.Map;<a name="line.12"></a>
<FONT color="green">013</FONT>    import javax.xml.bind.JAXBContext;<a name="line.13"></a>
<FONT color="green">014</FONT>    import javax.xml.bind.Marshaller;<a name="line.14"></a>
<FONT color="green">015</FONT>    import javax.xml.bind.Unmarshaller;<a name="line.15"></a>
<FONT color="green">016</FONT>    import edu.hawaii.myisern.collaborations.jaxb.Collaboration;<a name="line.16"></a>
<FONT color="green">017</FONT>    import edu.hawaii.myisern.collaborations.jaxb.Collaborations;<a name="line.17"></a>
<FONT color="green">018</FONT>    import edu.hawaii.myisern.organizations.jaxb.Organization;<a name="line.18"></a>
<FONT color="green">019</FONT>    import edu.hawaii.myisern.organizations.jaxb.Organizations;<a name="line.19"></a>
<FONT color="green">020</FONT>    import edu.hawaii.myisern.researchers.jaxb.Researcher;<a name="line.20"></a>
<FONT color="green">021</FONT>    import edu.hawaii.myisern.researchers.jaxb.Researchers;<a name="line.21"></a>
<FONT color="green">022</FONT>    <a name="line.22"></a>
<FONT color="green">023</FONT>    /**<a name="line.23"></a>
<FONT color="green">024</FONT>     * A Java class presentation of the ISERN social network. This class converts the XML files to the<a name="line.24"></a>
<FONT color="green">025</FONT>     * Java classes instances.<a name="line.25"></a>
<FONT color="green">026</FONT>     * <a name="line.26"></a>
<FONT color="green">027</FONT>     * @author Ed Kim<a name="line.27"></a>
<FONT color="green">028</FONT>     * @author Jon Lao<a name="line.28"></a>
<FONT color="green">029</FONT>     * @author Jianfei Liao<a name="line.29"></a>
<FONT color="green">030</FONT>     * @author Jared Sunouchi<a name="line.30"></a>
<FONT color="green">031</FONT>     */<a name="line.31"></a>
<FONT color="green">032</FONT>    public class MyIsernModel {<a name="line.32"></a>
<FONT color="green">033</FONT>      /** The singleton MyIsernModel instance. */<a name="line.33"></a>
<FONT color="green">034</FONT>      private static MyIsernModel theInstance = new MyIsernModel();<a name="line.34"></a>
<FONT color="green">035</FONT>    <a name="line.35"></a>
<FONT color="green">036</FONT>      /** Holds the class-wide JAXBContext, which is thread-safe. */<a name="line.36"></a>
<FONT color="green">037</FONT>      private JAXBContext collaborationsJaxbContext;<a name="line.37"></a>
<FONT color="green">038</FONT>      /** Holds the class-wide JAXBContext, which is thread-safe. */<a name="line.38"></a>
<FONT color="green">039</FONT>      private JAXBContext organizationsJaxbContext;<a name="line.39"></a>
<FONT color="green">040</FONT>      /** Holds the class-wide JAXBContext, which is thread-safe. */<a name="line.40"></a>
<FONT color="green">041</FONT>      private JAXBContext researchersJaxbContext;<a name="line.41"></a>
<FONT color="green">042</FONT>    <a name="line.42"></a>
<FONT color="green">043</FONT>      /** Holds collaborations data. */<a name="line.43"></a>
<FONT color="green">044</FONT>      private Collaborations collaborations;<a name="line.44"></a>
<FONT color="green">045</FONT>      /** Holds organizations data. */<a name="line.45"></a>
<FONT color="green">046</FONT>      private Organizations organizations;<a name="line.46"></a>
<FONT color="green">047</FONT>      /** Holds researchers data. */<a name="line.47"></a>
<FONT color="green">048</FONT>      private Researchers researchers;<a name="line.48"></a>
<FONT color="green">049</FONT>      /** A String represents "user.home". */<a name="line.49"></a>
<FONT color="green">050</FONT>      private static final String USER_HOME = "user.home";<a name="line.50"></a>
<FONT color="green">051</FONT>      /** Holds the derby database with the researchers. */<a name="line.51"></a>
<FONT color="green">052</FONT>      private DerbyPersistentStore db = new DerbyPersistentStore();<a name="line.52"></a>
<FONT color="green">053</FONT>    <a name="line.53"></a>
<FONT color="green">054</FONT>      /**<a name="line.54"></a>
<FONT color="green">055</FONT>       * Initializes this instance.<a name="line.55"></a>
<FONT color="green">056</FONT>       */<a name="line.56"></a>
<FONT color="green">057</FONT>      private MyIsernModel() {<a name="line.57"></a>
<FONT color="green">058</FONT>        try {<a name="line.58"></a>
<FONT color="green">059</FONT>          // try to read data from the database<a name="line.59"></a>
<FONT color="green">060</FONT>          System.out.println("Reading data from the database tables.");<a name="line.60"></a>
<FONT color="green">061</FONT>          this.researchers = this.db.getResearchers();<a name="line.61"></a>
<FONT color="green">062</FONT>          this.organizations = this.db.getOrganizations();<a name="line.62"></a>
<FONT color="green">063</FONT>          this.collaborations = this.db.getCollaborations();<a name="line.63"></a>
<FONT color="green">064</FONT>          <a name="line.64"></a>
<FONT color="green">065</FONT>          // if the database tables do not exist, import the XML files<a name="line.65"></a>
<FONT color="green">066</FONT>          String directory = System.getProperty(USER_HOME);<a name="line.66"></a>
<FONT color="green">067</FONT>          if (this.researchers == null || <a name="line.67"></a>
<FONT color="green">068</FONT>              this.organizations == null ||<a name="line.68"></a>
<FONT color="green">069</FONT>              this.collaborations == null) {<a name="line.69"></a>
<FONT color="green">070</FONT>            System.out.println("Database tables do not exist.");<a name="line.70"></a>
<FONT color="green">071</FONT>            this.importResearchersXml(directory + "/.myisern/researchers.black.xml");<a name="line.71"></a>
<FONT color="green">072</FONT>            this.importOrganizationsXml(directory + "/.myisern/organizations.black.xml");<a name="line.72"></a>
<FONT color="green">073</FONT>            this.importCollaborationsXml(directory + "/.myisern/collaborations.black.xml");<a name="line.73"></a>
<FONT color="green">074</FONT>    <a name="line.74"></a>
<FONT color="green">075</FONT>            // create the database tables<a name="line.75"></a>
<FONT color="green">076</FONT>            this.createTables();<a name="line.76"></a>
<FONT color="green">077</FONT>          }    <a name="line.77"></a>
<FONT color="green">078</FONT>        }<a name="line.78"></a>
<FONT color="green">079</FONT>        catch (Exception e) {<a name="line.79"></a>
<FONT color="green">080</FONT>          e.printStackTrace();<a name="line.80"></a>
<FONT color="green">081</FONT>        }<a name="line.81"></a>
<FONT color="green">082</FONT>      }<a name="line.82"></a>
<FONT color="green">083</FONT>      <a name="line.83"></a>
<FONT color="green">084</FONT>      /**<a name="line.84"></a>
<FONT color="green">085</FONT>       * Creates the database tables.<a name="line.85"></a>
<FONT color="green">086</FONT>       * <a name="line.86"></a>
<FONT color="green">087</FONT>       * @return true if the tables are created, false otherwise.<a name="line.87"></a>
<FONT color="green">088</FONT>       */<a name="line.88"></a>
<FONT color="green">089</FONT>      protected boolean createTables() {<a name="line.89"></a>
<FONT color="green">090</FONT>        boolean isWritten;<a name="line.90"></a>
<FONT color="green">091</FONT>        // create the database tables<a name="line.91"></a>
<FONT color="green">092</FONT>        System.out.println("Writing database tables.");<a name="line.92"></a>
<FONT color="green">093</FONT>        try {<a name="line.93"></a>
<FONT color="green">094</FONT>          this.db.writeResearchers(this.researchers);<a name="line.94"></a>
<FONT color="green">095</FONT>          this.db.writeOrganizations(this.organizations);<a name="line.95"></a>
<FONT color="green">096</FONT>          this.db.writeCollaborations(this.collaborations);<a name="line.96"></a>
<FONT color="green">097</FONT>          isWritten = true;<a name="line.97"></a>
<FONT color="green">098</FONT>        }<a name="line.98"></a>
<FONT color="green">099</FONT>        catch (Exception e) {<a name="line.99"></a>
<FONT color="green">100</FONT>          e.printStackTrace();<a name="line.100"></a>
<FONT color="green">101</FONT>          isWritten = false;<a name="line.101"></a>
<FONT color="green">102</FONT>        }<a name="line.102"></a>
<FONT color="green">103</FONT>        return isWritten;<a name="line.103"></a>
<FONT color="green">104</FONT>      }<a name="line.104"></a>
<FONT color="green">105</FONT>    <a name="line.105"></a>
<FONT color="green">106</FONT>      /**<a name="line.106"></a>
<FONT color="green">107</FONT>       * Gets the single instance of MyIsernModel object.<a name="line.107"></a>
<FONT color="green">108</FONT>       * <a name="line.108"></a>
<FONT color="green">109</FONT>       * @return A MyIsernModel.<a name="line.109"></a>
<FONT color="green">110</FONT>       */<a name="line.110"></a>
<FONT color="green">111</FONT>      public static synchronized MyIsernModel getInstance() {<a name="line.111"></a>
<FONT color="green">112</FONT>        return MyIsernModel.theInstance;<a name="line.112"></a>
<FONT color="green">113</FONT>      }<a name="line.113"></a>
<FONT color="green">114</FONT>    <a name="line.114"></a>
<FONT color="green">115</FONT>      /**<a name="line.115"></a>
<FONT color="green">116</FONT>       * Makes an unique ID using the name.<a name="line.116"></a>
<FONT color="green">117</FONT>       * <a name="line.117"></a>
<FONT color="green">118</FONT>       * @param name The name that is used to make the unique ID.<a name="line.118"></a>
<FONT color="green">119</FONT>       * @return The unique ID.<a name="line.119"></a>
<FONT color="green">120</FONT>       */<a name="line.120"></a>
<FONT color="green">121</FONT>      public synchronized String makeId(String name) {<a name="line.121"></a>
<FONT color="green">122</FONT>        String id = name.replace(' ', '_');<a name="line.122"></a>
<FONT color="green">123</FONT>        return id;<a name="line.123"></a>
<FONT color="green">124</FONT>      }<a name="line.124"></a>
<FONT color="green">125</FONT>      <a name="line.125"></a>
<FONT color="green">126</FONT>      /**<a name="line.126"></a>
<FONT color="green">127</FONT>       * Gets all the researchers as a map<a name="line.127"></a>
<FONT color="green">128</FONT>       * <a name="line.128"></a>
<FONT color="green">129</FONT>       * @return researchers map<a name="line.129"></a>
<FONT color="green">130</FONT>       */<a name="line.130"></a>
<FONT color="green">131</FONT>      public synchronized Map&lt;String, Researcher&gt; getResearchersMap() {<a name="line.131"></a>
<FONT color="green">132</FONT>        Map&lt;String, Researcher&gt; map = new HashMap&lt;String, Researcher&gt;();<a name="line.132"></a>
<FONT color="green">133</FONT>        String id = null;<a name="line.133"></a>
<FONT color="green">134</FONT>        for (Researcher tempResearcher : this.researchers.getResearcher()) {<a name="line.134"></a>
<FONT color="green">135</FONT>          id = this.makeId(tempResearcher.getName());<a name="line.135"></a>
<FONT color="green">136</FONT>          map.put(id, tempResearcher);<a name="line.136"></a>
<FONT color="green">137</FONT>        }<a name="line.137"></a>
<FONT color="green">138</FONT>        return map;<a name="line.138"></a>
<FONT color="green">139</FONT>      }<a name="line.139"></a>
<FONT color="green">140</FONT>    <a name="line.140"></a>
<FONT color="green">141</FONT>      /**<a name="line.141"></a>
<FONT color="green">142</FONT>       * Gets all the organizations as a map<a name="line.142"></a>
<FONT color="green">143</FONT>       * <a name="line.143"></a>
<FONT color="green">144</FONT>       * @return organizations map<a name="line.144"></a>
<FONT color="green">145</FONT>       */<a name="line.145"></a>
<FONT color="green">146</FONT>      public synchronized Map&lt;String, Organization&gt; getOrganizationsMap() {<a name="line.146"></a>
<FONT color="green">147</FONT>        Map&lt;String, Organization&gt; map = new HashMap&lt;String, Organization&gt;();<a name="line.147"></a>
<FONT color="green">148</FONT>        String id = null;<a name="line.148"></a>
<FONT color="green">149</FONT>        for (Organization tempOrg : this.organizations.getOrganization()) {<a name="line.149"></a>
<FONT color="green">150</FONT>          id = this.makeId(tempOrg.getName());<a name="line.150"></a>
<FONT color="green">151</FONT>          map.put(id, tempOrg);<a name="line.151"></a>
<FONT color="green">152</FONT>        }<a name="line.152"></a>
<FONT color="green">153</FONT>        return map;<a name="line.153"></a>
<FONT color="green">154</FONT>      }<a name="line.154"></a>
<FONT color="green">155</FONT>    <a name="line.155"></a>
<FONT color="green">156</FONT>      /**<a name="line.156"></a>
<FONT color="green">157</FONT>       * Get all the collaborations as a map<a name="line.157"></a>
<FONT color="green">158</FONT>       * <a name="line.158"></a>
<FONT color="green">159</FONT>       * @return collaborations map<a name="line.159"></a>
<FONT color="green">160</FONT>       */<a name="line.160"></a>
<FONT color="green">161</FONT>      public synchronized Map&lt;String, Collaboration&gt; getCollaborationsMap() {<a name="line.161"></a>
<FONT color="green">162</FONT>        Map&lt;String, Collaboration&gt; map = new HashMap&lt;String, Collaboration&gt;();<a name="line.162"></a>
<FONT color="green">163</FONT>        String id = null;<a name="line.163"></a>
<FONT color="green">164</FONT>        for (Collaboration tempCollab : this.collaborations.getCollaboration()) {<a name="line.164"></a>
<FONT color="green">165</FONT>          id = this.makeId(tempCollab.getName());<a name="line.165"></a>
<FONT color="green">166</FONT>          map.put(id, tempCollab);<a name="line.166"></a>
<FONT color="green">167</FONT>        }<a name="line.167"></a>
<FONT color="green">168</FONT>        return map;<a name="line.168"></a>
<FONT color="green">169</FONT>      }<a name="line.169"></a>
<FONT color="green">170</FONT>    <a name="line.170"></a>
<FONT color="green">171</FONT>      /**<a name="line.171"></a>
<FONT color="green">172</FONT>       * Gets a single researcher<a name="line.172"></a>
<FONT color="green">173</FONT>       * <a name="line.173"></a>
<FONT color="green">174</FONT>       * @param name The name of the researcher<a name="line.174"></a>
<FONT color="green">175</FONT>       * @return a single researcher<a name="line.175"></a>
<FONT color="green">176</FONT>       */<a name="line.176"></a>
<FONT color="green">177</FONT>      public synchronized Researcher getSingleResearcher(String name) {<a name="line.177"></a>
<FONT color="green">178</FONT>        return this.getResearchersMap().get(this.makeId(name));<a name="line.178"></a>
<FONT color="green">179</FONT>      }<a name="line.179"></a>
<FONT color="green">180</FONT>    <a name="line.180"></a>
<FONT color="green">181</FONT>      /**<a name="line.181"></a>
<FONT color="green">182</FONT>       * Gets a single organization<a name="line.182"></a>
<FONT color="green">183</FONT>       * <a name="line.183"></a>
<FONT color="green">184</FONT>       * @param name The name of the organization<a name="line.184"></a>
<FONT color="green">185</FONT>       * @return a single organization<a name="line.185"></a>
<FONT color="green">186</FONT>       */<a name="line.186"></a>
<FONT color="green">187</FONT>      public synchronized Organization getSingleOrganization(String name) {<a name="line.187"></a>
<FONT color="green">188</FONT>        return this.getOrganizationsMap().get(this.makeId(name));<a name="line.188"></a>
<FONT color="green">189</FONT>      }<a name="line.189"></a>
<FONT color="green">190</FONT>    <a name="line.190"></a>
<FONT color="green">191</FONT>      /**<a name="line.191"></a>
<FONT color="green">192</FONT>       * Gets a single collaboration<a name="line.192"></a>
<FONT color="green">193</FONT>       * <a name="line.193"></a>
<FONT color="green">194</FONT>       * @param name The name of the collaboration<a name="line.194"></a>
<FONT color="green">195</FONT>       * @return a single collaboration<a name="line.195"></a>
<FONT color="green">196</FONT>       */<a name="line.196"></a>
<FONT color="green">197</FONT>      public synchronized Collaboration getSingleCollaboration(String name) {<a name="line.197"></a>
<FONT color="green">198</FONT>        return this.getCollaborationsMap().get(this.makeId(name));<a name="line.198"></a>
<FONT color="green">199</FONT>      }<a name="line.199"></a>
<FONT color="green">200</FONT>    <a name="line.200"></a>
<FONT color="green">201</FONT>      /**<a name="line.201"></a>
<FONT color="green">202</FONT>       * Gets all the researchers as a list<a name="line.202"></a>
<FONT color="green">203</FONT>       * <a name="line.203"></a>
<FONT color="green">204</FONT>       * @return A list containing all the researchers.<a name="line.204"></a>
<FONT color="green">205</FONT>       */<a name="line.205"></a>
<FONT color="green">206</FONT>      public synchronized List&lt;Researcher&gt; getResearchersList() {<a name="line.206"></a>
<FONT color="green">207</FONT>        return this.researchers.getResearcher();<a name="line.207"></a>
<FONT color="green">208</FONT>      }<a name="line.208"></a>
<FONT color="green">209</FONT>    <a name="line.209"></a>
<FONT color="green">210</FONT>      /**<a name="line.210"></a>
<FONT color="green">211</FONT>       * Gets all the organizations as a list<a name="line.211"></a>
<FONT color="green">212</FONT>       * <a name="line.212"></a>
<FONT color="green">213</FONT>       * @return A list containing all the organizations.<a name="line.213"></a>
<FONT color="green">214</FONT>       */<a name="line.214"></a>
<FONT color="green">215</FONT>      public synchronized List&lt;Organization&gt; getOrganizationsList() {<a name="line.215"></a>
<FONT color="green">216</FONT>        return this.organizations.getOrganization();<a name="line.216"></a>
<FONT color="green">217</FONT>      }<a name="line.217"></a>
<FONT color="green">218</FONT>    <a name="line.218"></a>
<FONT color="green">219</FONT>      /**<a name="line.219"></a>
<FONT color="green">220</FONT>       * Gets all the collaborations as a list<a name="line.220"></a>
<FONT color="green">221</FONT>       * <a name="line.221"></a>
<FONT color="green">222</FONT>       * @return A list containing all the collaborations.<a name="line.222"></a>
<FONT color="green">223</FONT>       */<a name="line.223"></a>
<FONT color="green">224</FONT>      public synchronized List&lt;Collaboration&gt; getCollaborationsList() {<a name="line.224"></a>
<FONT color="green">225</FONT>        return this.collaborations.getCollaboration();<a name="line.225"></a>
<FONT color="green">226</FONT>      }<a name="line.226"></a>
<FONT color="green">227</FONT>      <a name="line.227"></a>
<FONT color="green">228</FONT>      /**<a name="line.228"></a>
<FONT color="green">229</FONT>       * Adds or edits a researcher.<a name="line.229"></a>
<FONT color="green">230</FONT>       * <a name="line.230"></a>
<FONT color="green">231</FONT>       * @param researcher The researcher to be added or edited.<a name="line.231"></a>
<FONT color="green">232</FONT>       * @return The Researchers object after the adding or editing.<a name="line.232"></a>
<FONT color="green">233</FONT>       */<a name="line.233"></a>
<FONT color="green">234</FONT>      public synchronized Researchers addOrEditResearcher(Researcher researcher) {<a name="line.234"></a>
<FONT color="green">235</FONT>        // get the unique ID<a name="line.235"></a>
<FONT color="green">236</FONT>        String id = this.makeId(researcher.getName());<a name="line.236"></a>
<FONT color="green">237</FONT>        // if the researcher already exists<a name="line.237"></a>
<FONT color="green">238</FONT>        if (this.getResearchersMap().containsKey(id)) {<a name="line.238"></a>
<FONT color="green">239</FONT>          Researcher tempResearcher = this.getResearchersMap().get(id);<a name="line.239"></a>
<FONT color="green">240</FONT>          // construct a new Researchers object without the old researcher<a name="line.240"></a>
<FONT color="green">241</FONT>          int index = this.getResearchersList().indexOf(tempResearcher);<a name="line.241"></a>
<FONT color="green">242</FONT>          List&lt;Researcher&gt; list = this.getResearchersList();<a name="line.242"></a>
<FONT color="green">243</FONT>          list.set(index, researcher);<a name="line.243"></a>
<FONT color="green">244</FONT>          Researchers researchers = new Researchers();<a name="line.244"></a>
<FONT color="green">245</FONT>          researchers.getResearcher().addAll(list);<a name="line.245"></a>
<FONT color="green">246</FONT>          this.researchers = researchers;<a name="line.246"></a>
<FONT color="green">247</FONT>          // update database<a name="line.247"></a>
<FONT color="green">248</FONT>          this.db.updateResearcher(researcher);<a name="line.248"></a>
<FONT color="green">249</FONT>        }<a name="line.249"></a>
<FONT color="green">250</FONT>        // if the researcher is new<a name="line.250"></a>
<FONT color="green">251</FONT>        else {<a name="line.251"></a>
<FONT color="green">252</FONT>          this.researchers.getResearcher().add(researcher);<a name="line.252"></a>
<FONT color="green">253</FONT>          // update database<a name="line.253"></a>
<FONT color="green">254</FONT>          this.db.insertResearcher(researcher);<a name="line.254"></a>
<FONT color="green">255</FONT>        }<a name="line.255"></a>
<FONT color="green">256</FONT>        <a name="line.256"></a>
<FONT color="green">257</FONT>        return this.researchers;<a name="line.257"></a>
<FONT color="green">258</FONT>      }<a name="line.258"></a>
<FONT color="green">259</FONT>    <a name="line.259"></a>
<FONT color="green">260</FONT>      /**<a name="line.260"></a>
<FONT color="green">261</FONT>       * Adds or edits an organization.<a name="line.261"></a>
<FONT color="green">262</FONT>       * <a name="line.262"></a>
<FONT color="green">263</FONT>       * @param organization The organization to be added or edited.<a name="line.263"></a>
<FONT color="green">264</FONT>       * @return The Organizations object after the adding or editing.<a name="line.264"></a>
<FONT color="green">265</FONT>       */<a name="line.265"></a>
<FONT color="green">266</FONT>      public synchronized Organizations addOrEditOrganization(Organization organization) {<a name="line.266"></a>
<FONT color="green">267</FONT>        // get the unique ID<a name="line.267"></a>
<FONT color="green">268</FONT>        String id = this.makeId(organization.getName());<a name="line.268"></a>
<FONT color="green">269</FONT>        // if the organization already exists<a name="line.269"></a>
<FONT color="green">270</FONT>        if (this.getOrganizationsMap().containsKey(id)) {<a name="line.270"></a>
<FONT color="green">271</FONT>          Organization tempOrganization = this.getOrganizationsMap().get(id);<a name="line.271"></a>
<FONT color="green">272</FONT>          // construct a new Organizations object without the old organization<a name="line.272"></a>
<FONT color="green">273</FONT>          int index = this.getOrganizationsList().indexOf(tempOrganization);<a name="line.273"></a>
<FONT color="green">274</FONT>          List&lt;Organization&gt; list = this.getOrganizationsList();<a name="line.274"></a>
<FONT color="green">275</FONT>          list.set(index, organization);<a name="line.275"></a>
<FONT color="green">276</FONT>          Organizations organizations = new Organizations();<a name="line.276"></a>
<FONT color="green">277</FONT>          organizations.getOrganization().addAll(list);<a name="line.277"></a>
<FONT color="green">278</FONT>          this.organizations = organizations;<a name="line.278"></a>
<FONT color="green">279</FONT>          // update database<a name="line.279"></a>
<FONT color="green">280</FONT>          this.db.updateOrganization(organization);<a name="line.280"></a>
<FONT color="green">281</FONT>        }<a name="line.281"></a>
<FONT color="green">282</FONT>        // if the organization is new<a name="line.282"></a>
<FONT color="green">283</FONT>        else {<a name="line.283"></a>
<FONT color="green">284</FONT>          this.organizations.getOrganization().add(organization);<a name="line.284"></a>
<FONT color="green">285</FONT>          // update database<a name="line.285"></a>
<FONT color="green">286</FONT>          this.db.insertOrganization(organization);<a name="line.286"></a>
<FONT color="green">287</FONT>        }<a name="line.287"></a>
<FONT color="green">288</FONT>    <a name="line.288"></a>
<FONT color="green">289</FONT>        return this.organizations;<a name="line.289"></a>
<FONT color="green">290</FONT>      }<a name="line.290"></a>
<FONT color="green">291</FONT>    <a name="line.291"></a>
<FONT color="green">292</FONT>      /**<a name="line.292"></a>
<FONT color="green">293</FONT>       * Adds or edits a researcher.<a name="line.293"></a>
<FONT color="green">294</FONT>       * <a name="line.294"></a>
<FONT color="green">295</FONT>       * @param collaboration The collaboration to be added or edited.<a name="line.295"></a>
<FONT color="green">296</FONT>       * @return The Collaborations object.<a name="line.296"></a>
<FONT color="green">297</FONT>       */<a name="line.297"></a>
<FONT color="green">298</FONT>      public synchronized Collaborations addOrEditCollaboration(Collaboration collaboration) {<a name="line.298"></a>
<FONT color="green">299</FONT>        // get the unique ID<a name="line.299"></a>
<FONT color="green">300</FONT>        String id = this.makeId(collaboration.getName());<a name="line.300"></a>
<FONT color="green">301</FONT>        // if the collaboration already exists<a name="line.301"></a>
<FONT color="green">302</FONT>        if (this.getCollaborationsMap().containsKey(id)) {<a name="line.302"></a>
<FONT color="green">303</FONT>          Collaboration tempCollaboration = this.getCollaborationsMap().get(id);<a name="line.303"></a>
<FONT color="green">304</FONT>          // construct a new Collaborations object without the old collaboration<a name="line.304"></a>
<FONT color="green">305</FONT>          int index = this.getCollaborationsList().indexOf(tempCollaboration);<a name="line.305"></a>
<FONT color="green">306</FONT>          List&lt;Collaboration&gt; list = this.getCollaborationsList();<a name="line.306"></a>
<FONT color="green">307</FONT>          list.set(index, collaboration);<a name="line.307"></a>
<FONT color="green">308</FONT>          Collaborations collaborations = new Collaborations();<a name="line.308"></a>
<FONT color="green">309</FONT>          collaborations.getCollaboration().addAll(list);<a name="line.309"></a>
<FONT color="green">310</FONT>          this.collaborations = collaborations;<a name="line.310"></a>
<FONT color="green">311</FONT>          // update database<a name="line.311"></a>
<FONT color="green">312</FONT>          this.db.updateCollaboration(collaboration);<a name="line.312"></a>
<FONT color="green">313</FONT>        }<a name="line.313"></a>
<FONT color="green">314</FONT>        // if the collaboration is new<a name="line.314"></a>
<FONT color="green">315</FONT>        else {<a name="line.315"></a>
<FONT color="green">316</FONT>          this.collaborations.getCollaboration().add(collaboration);<a name="line.316"></a>
<FONT color="green">317</FONT>          // update database<a name="line.317"></a>
<FONT color="green">318</FONT>          this.db.insertCollaboration(collaboration);<a name="line.318"></a>
<FONT color="green">319</FONT>        }<a name="line.319"></a>
<FONT color="green">320</FONT>        <a name="line.320"></a>
<FONT color="green">321</FONT>        return this.collaborations;<a name="line.321"></a>
<FONT color="green">322</FONT>      }<a name="line.322"></a>
<FONT color="green">323</FONT>      <a name="line.323"></a>
<FONT color="green">324</FONT>      /**<a name="line.324"></a>
<FONT color="green">325</FONT>       * Removes a researcher.<a name="line.325"></a>
<FONT color="green">326</FONT>       * <a name="line.326"></a>
<FONT color="green">327</FONT>       * @param name The name of the researcher to be removed.<a name="line.327"></a>
<FONT color="green">328</FONT>       * @return true if the researcher is deleted, false otherwise.<a name="line.328"></a>
<FONT color="green">329</FONT>       */<a name="line.329"></a>
<FONT color="green">330</FONT>      public synchronized boolean removeResearcher(String name) {<a name="line.330"></a>
<FONT color="green">331</FONT>        // find the researcher to remove<a name="line.331"></a>
<FONT color="green">332</FONT>        Researcher researcher = this.getSingleResearcher(name);<a name="line.332"></a>
<FONT color="green">333</FONT>        // try to remove it<a name="line.333"></a>
<FONT color="green">334</FONT>        if (this.researchers.getResearcher().remove(researcher)) {<a name="line.334"></a>
<FONT color="green">335</FONT>          db.removeResearcher(researcher);<a name="line.335"></a>
<FONT color="green">336</FONT>          return true;<a name="line.336"></a>
<FONT color="green">337</FONT>        }<a name="line.337"></a>
<FONT color="green">338</FONT>        return false;<a name="line.338"></a>
<FONT color="green">339</FONT>      }<a name="line.339"></a>
<FONT color="green">340</FONT>      <a name="line.340"></a>
<FONT color="green">341</FONT>      /**<a name="line.341"></a>
<FONT color="green">342</FONT>       * Removes an organization.<a name="line.342"></a>
<FONT color="green">343</FONT>       * <a name="line.343"></a>
<FONT color="green">344</FONT>       * @param name The name of the organization to be removed.<a name="line.344"></a>
<FONT color="green">345</FONT>       * @return true if the organization is deleted, false otherwise.<a name="line.345"></a>
<FONT color="green">346</FONT>       */<a name="line.346"></a>
<FONT color="green">347</FONT>      public synchronized boolean removeOrganization(String name) {<a name="line.347"></a>
<FONT color="green">348</FONT>        // find the organization to remove<a name="line.348"></a>
<FONT color="green">349</FONT>        Organization organization = this.getSingleOrganization(name);<a name="line.349"></a>
<FONT color="green">350</FONT>        // try to remove it<a name="line.350"></a>
<FONT color="green">351</FONT>        if (this.organizations.getOrganization().remove(organization)) {<a name="line.351"></a>
<FONT color="green">352</FONT>          db.removeOrganization(organization);<a name="line.352"></a>
<FONT color="green">353</FONT>          return true;<a name="line.353"></a>
<FONT color="green">354</FONT>        }<a name="line.354"></a>
<FONT color="green">355</FONT>        return false;<a name="line.355"></a>
<FONT color="green">356</FONT>      }<a name="line.356"></a>
<FONT color="green">357</FONT>      <a name="line.357"></a>
<FONT color="green">358</FONT>      /**<a name="line.358"></a>
<FONT color="green">359</FONT>       * Removes a collaboration.<a name="line.359"></a>
<FONT color="green">360</FONT>       * <a name="line.360"></a>
<FONT color="green">361</FONT>       * @param name The name of the collaboration to be removed.<a name="line.361"></a>
<FONT color="green">362</FONT>       * @return true if the collaboration is deleted, false otherwise.<a name="line.362"></a>
<FONT color="green">363</FONT>       */<a name="line.363"></a>
<FONT color="green">364</FONT>      public synchronized boolean removeCollaboration(String name) {<a name="line.364"></a>
<FONT color="green">365</FONT>        // find the collaboration to remove<a name="line.365"></a>
<FONT color="green">366</FONT>        Collaboration collaboration = this.getSingleCollaboration(name);<a name="line.366"></a>
<FONT color="green">367</FONT>        // try to remove it<a name="line.367"></a>
<FONT color="green">368</FONT>        if (this.collaborations.getCollaboration().remove(collaboration)) {<a name="line.368"></a>
<FONT color="green">369</FONT>          db.removeCollaboration(collaboration);<a name="line.369"></a>
<FONT color="green">370</FONT>          return true;<a name="line.370"></a>
<FONT color="green">371</FONT>        }<a name="line.371"></a>
<FONT color="green">372</FONT>        return false;<a name="line.372"></a>
<FONT color="green">373</FONT>      }<a name="line.373"></a>
<FONT color="green">374</FONT>      <a name="line.374"></a>
<FONT color="green">375</FONT>      /**<a name="line.375"></a>
<FONT color="green">376</FONT>       * Sorts the researchers by name.<a name="line.376"></a>
<FONT color="green">377</FONT>       */<a name="line.377"></a>
<FONT color="green">378</FONT>      public synchronized void sortResearchers() {<a name="line.378"></a>
<FONT color="green">379</FONT>        List&lt;Researcher&gt; rNames = this.researchers.getResearcher();<a name="line.379"></a>
<FONT color="green">380</FONT>        <a name="line.380"></a>
<FONT color="green">381</FONT>        List&lt;String&gt; names = new ArrayList&lt;String&gt;();<a name="line.381"></a>
<FONT color="green">382</FONT>        for (Researcher res : rNames) {<a name="line.382"></a>
<FONT color="green">383</FONT>          names.add(res.getName());<a name="line.383"></a>
<FONT color="green">384</FONT>        }<a name="line.384"></a>
<FONT color="green">385</FONT>        <a name="line.385"></a>
<FONT color="green">386</FONT>        Collections.sort(names);<a name="line.386"></a>
<FONT color="green">387</FONT>        List&lt;Researcher&gt; sortedResearchers = new ArrayList&lt;Researcher&gt;();<a name="line.387"></a>
<FONT color="green">388</FONT>        for (String name : names) {<a name="line.388"></a>
<FONT color="green">389</FONT>          for (Researcher res : rNames) {<a name="line.389"></a>
<FONT color="green">390</FONT>            if (name.equals(res.getName())) {<a name="line.390"></a>
<FONT color="green">391</FONT>              sortedResearchers.add(res);<a name="line.391"></a>
<FONT color="green">392</FONT>            }<a name="line.392"></a>
<FONT color="green">393</FONT>          }<a name="line.393"></a>
<FONT color="green">394</FONT>        }<a name="line.394"></a>
<FONT color="green">395</FONT>        this.researchers.getResearcher().clear();<a name="line.395"></a>
<FONT color="green">396</FONT>        this.researchers.getResearcher().addAll(sortedResearchers);<a name="line.396"></a>
<FONT color="green">397</FONT>      }<a name="line.397"></a>
<FONT color="green">398</FONT>      <a name="line.398"></a>
<FONT color="green">399</FONT>      /**<a name="line.399"></a>
<FONT color="green">400</FONT>       * Sorts the organizations by name.<a name="line.400"></a>
<FONT color="green">401</FONT>       */<a name="line.401"></a>
<FONT color="green">402</FONT>      public synchronized void sortOrganizations() {<a name="line.402"></a>
<FONT color="green">403</FONT>        List&lt;Organization&gt; oNames = this.organizations.getOrganization();<a name="line.403"></a>
<FONT color="green">404</FONT>        <a name="line.404"></a>
<FONT color="green">405</FONT>        List&lt;String&gt; names = new ArrayList&lt;String&gt;();<a name="line.405"></a>
<FONT color="green">406</FONT>        for (Organization org : oNames) {<a name="line.406"></a>
<FONT color="green">407</FONT>          names.add(org.getName());<a name="line.407"></a>
<FONT color="green">408</FONT>        }<a name="line.408"></a>
<FONT color="green">409</FONT>        <a name="line.409"></a>
<FONT color="green">410</FONT>        Collections.sort(names);<a name="line.410"></a>
<FONT color="green">411</FONT>        List&lt;Organization&gt; sortedOrganizations = new ArrayList&lt;Organization&gt;();<a name="line.411"></a>
<FONT color="green">412</FONT>        for (String name : names) {<a name="line.412"></a>
<FONT color="green">413</FONT>          for (Organization org : oNames) {<a name="line.413"></a>
<FONT color="green">414</FONT>            if (name.equals(org.getName())) {<a name="line.414"></a>
<FONT color="green">415</FONT>              sortedOrganizations.add(org);<a name="line.415"></a>
<FONT color="green">416</FONT>            }<a name="line.416"></a>
<FONT color="green">417</FONT>          }<a name="line.417"></a>
<FONT color="green">418</FONT>        }<a name="line.418"></a>
<FONT color="green">419</FONT>        this.organizations.getOrganization().clear();<a name="line.419"></a>
<FONT color="green">420</FONT>        this.organizations.getOrganization().addAll(sortedOrganizations);<a name="line.420"></a>
<FONT color="green">421</FONT>      }<a name="line.421"></a>
<FONT color="green">422</FONT>      <a name="line.422"></a>
<FONT color="green">423</FONT>      /**<a name="line.423"></a>
<FONT color="green">424</FONT>       * Sorts the collaborations by name.<a name="line.424"></a>
<FONT color="green">425</FONT>       */<a name="line.425"></a>
<FONT color="green">426</FONT>      public synchronized void sortCollaborations() {<a name="line.426"></a>
<FONT color="green">427</FONT>        List&lt;Collaboration&gt; cNames = this.collaborations.getCollaboration();<a name="line.427"></a>
<FONT color="green">428</FONT>        <a name="line.428"></a>
<FONT color="green">429</FONT>        List&lt;String&gt; names = new ArrayList&lt;String&gt;();<a name="line.429"></a>
<FONT color="green">430</FONT>        for (Collaboration collab : cNames) {<a name="line.430"></a>
<FONT color="green">431</FONT>          names.add(collab.getName());<a name="line.431"></a>
<FONT color="green">432</FONT>        }<a name="line.432"></a>
<FONT color="green">433</FONT>        <a name="line.433"></a>
<FONT color="green">434</FONT>        Collections.sort(names);<a name="line.434"></a>
<FONT color="green">435</FONT>        List&lt;Collaboration&gt; sortedCollaborations = new ArrayList&lt;Collaboration&gt;();<a name="line.435"></a>
<FONT color="green">436</FONT>        for (String name : names ) {<a name="line.436"></a>
<FONT color="green">437</FONT>          for (Collaboration collab : cNames) {<a name="line.437"></a>
<FONT color="green">438</FONT>            if (name.equals(collab.getName())) {<a name="line.438"></a>
<FONT color="green">439</FONT>              sortedCollaborations.add(collab);<a name="line.439"></a>
<FONT color="green">440</FONT>            }<a name="line.440"></a>
<FONT color="green">441</FONT>          }<a name="line.441"></a>
<FONT color="green">442</FONT>        }<a name="line.442"></a>
<FONT color="green">443</FONT>        this.collaborations.getCollaboration().clear();<a name="line.443"></a>
<FONT color="green">444</FONT>        this.collaborations.getCollaboration().addAll(sortedCollaborations);<a name="line.444"></a>
<FONT color="green">445</FONT>      }<a name="line.445"></a>
<FONT color="green">446</FONT>      <a name="line.446"></a>
<FONT color="green">447</FONT>      /**<a name="line.447"></a>
<FONT color="green">448</FONT>       * Creates and returns the list of researcher names.<a name="line.448"></a>
<FONT color="green">449</FONT>       * <a name="line.449"></a>
<FONT color="green">450</FONT>       * @return The list of researcher names.<a name="line.450"></a>
<FONT color="green">451</FONT>       */<a name="line.451"></a>
<FONT color="green">452</FONT>      public synchronized List&lt;String&gt; getResearcherNames() {<a name="line.452"></a>
<FONT color="green">453</FONT>        List&lt;Researcher&gt; researcherList = this.getResearchersList();<a name="line.453"></a>
<FONT color="green">454</FONT>        List&lt;String&gt; researcherNamesList = new ArrayList&lt;String&gt;();<a name="line.454"></a>
<FONT color="green">455</FONT>        for (Researcher res : researcherList) {<a name="line.455"></a>
<FONT color="green">456</FONT>          researcherNamesList.add(res.getName());<a name="line.456"></a>
<FONT color="green">457</FONT>        }<a name="line.457"></a>
<FONT color="green">458</FONT>        Collections.sort(researcherNamesList);<a name="line.458"></a>
<FONT color="green">459</FONT>        <a name="line.459"></a>
<FONT color="green">460</FONT>        return researcherNamesList;<a name="line.460"></a>
<FONT color="green">461</FONT>      }<a name="line.461"></a>
<FONT color="green">462</FONT>        <a name="line.462"></a>
<FONT color="green">463</FONT>      /**<a name="line.463"></a>
<FONT color="green">464</FONT>       * Returns the string representation that will be used to generate the javascript array.<a name="line.464"></a>
<FONT color="green">465</FONT>       * <a name="line.465"></a>
<FONT color="green">466</FONT>       * @return The string representation that will be used to generate the javascript array. <a name="line.466"></a>
<FONT color="green">467</FONT>       */<a name="line.467"></a>
<FONT color="green">468</FONT>      public synchronized String getResearcherNamesList() {<a name="line.468"></a>
<FONT color="green">469</FONT>        List&lt;String&gt; list = getResearcherNames();<a name="line.469"></a>
<FONT color="green">470</FONT>        String delimiter = "|";<a name="line.470"></a>
<FONT color="green">471</FONT>        StringBuffer names = new StringBuffer();<a name="line.471"></a>
<FONT color="green">472</FONT>        for (String name : list) {<a name="line.472"></a>
<FONT color="green">473</FONT>          names.append(name);<a name="line.473"></a>
<FONT color="green">474</FONT>          names.append(delimiter);<a name="line.474"></a>
<FONT color="green">475</FONT>        }<a name="line.475"></a>
<FONT color="green">476</FONT>    <a name="line.476"></a>
<FONT color="green">477</FONT>        return names.substring(0, (names.length() - 1));<a name="line.477"></a>
<FONT color="green">478</FONT>      }<a name="line.478"></a>
<FONT color="green">479</FONT>      <a name="line.479"></a>
<FONT color="green">480</FONT>      /**<a name="line.480"></a>
<FONT color="green">481</FONT>       * Creates and returns the list of organization names.<a name="line.481"></a>
<FONT color="green">482</FONT>       * <a name="line.482"></a>
<FONT color="green">483</FONT>       * @return The list of organization names.<a name="line.483"></a>
<FONT color="green">484</FONT>       */<a name="line.484"></a>
<FONT color="green">485</FONT>      public synchronized List&lt;String&gt; getOrganizationNames() {<a name="line.485"></a>
<FONT color="green">486</FONT>        List&lt;Organization&gt; organizationList = getOrganizationsList();<a name="line.486"></a>
<FONT color="green">487</FONT>        List&lt;String&gt; organizationNamesList = new ArrayList&lt;String&gt;();<a name="line.487"></a>
<FONT color="green">488</FONT>        for (Organization org : organizationList) {<a name="line.488"></a>
<FONT color="green">489</FONT>          organizationNamesList.add(org.getName());<a name="line.489"></a>
<FONT color="green">490</FONT>        }<a name="line.490"></a>
<FONT color="green">491</FONT>        Collections.sort(organizationNamesList);<a name="line.491"></a>
<FONT color="green">492</FONT>        <a name="line.492"></a>
<FONT color="green">493</FONT>        return organizationNamesList;<a name="line.493"></a>
<FONT color="green">494</FONT>      }<a name="line.494"></a>
<FONT color="green">495</FONT>        <a name="line.495"></a>
<FONT color="green">496</FONT>      /**<a name="line.496"></a>
<FONT color="green">497</FONT>       * Returns the string representation that will be used to generate the javascript array.<a name="line.497"></a>
<FONT color="green">498</FONT>       * <a name="line.498"></a>
<FONT color="green">499</FONT>       * @return The string representation that will be used to generate the javascript array. <a name="line.499"></a>
<FONT color="green">500</FONT>       */<a name="line.500"></a>
<FONT color="green">501</FONT>      public synchronized String getOrganizationNamesList() {<a name="line.501"></a>
<FONT color="green">502</FONT>        List&lt;String&gt; list = getOrganizationNames();<a name="line.502"></a>
<FONT color="green">503</FONT>        String delimiter = "|";<a name="line.503"></a>
<FONT color="green">504</FONT>        StringBuffer names = new StringBuffer();<a name="line.504"></a>
<FONT color="green">505</FONT>        for (String name : list) {<a name="line.505"></a>
<FONT color="green">506</FONT>          names.append(name);<a name="line.506"></a>
<FONT color="green">507</FONT>          names.append(delimiter);<a name="line.507"></a>
<FONT color="green">508</FONT>        }<a name="line.508"></a>
<FONT color="green">509</FONT>    <a name="line.509"></a>
<FONT color="green">510</FONT>        return names.substring(0, (names.length() - 1));<a name="line.510"></a>
<FONT color="green">511</FONT>      }<a name="line.511"></a>
<FONT color="green">512</FONT>      <a name="line.512"></a>
<FONT color="green">513</FONT>      /**<a name="line.513"></a>
<FONT color="green">514</FONT>       * Creates and returns the list of collaboration names.<a name="line.514"></a>
<FONT color="green">515</FONT>       * <a name="line.515"></a>
<FONT color="green">516</FONT>       * @return The list of collaboration names.<a name="line.516"></a>
<FONT color="green">517</FONT>       */<a name="line.517"></a>
<FONT color="green">518</FONT>      public synchronized List&lt;String&gt; getCollaborationNames() {<a name="line.518"></a>
<FONT color="green">519</FONT>        List&lt;Collaboration&gt; collaborationList = getCollaborationsList();<a name="line.519"></a>
<FONT color="green">520</FONT>        List&lt;String&gt; collaborationNamesList = new ArrayList&lt;String&gt;();<a name="line.520"></a>
<FONT color="green">521</FONT>        for (Collaboration collab : collaborationList) {<a name="line.521"></a>
<FONT color="green">522</FONT>          collaborationNamesList.add(collab.getName());<a name="line.522"></a>
<FONT color="green">523</FONT>        }<a name="line.523"></a>
<FONT color="green">524</FONT>        Collections.sort(collaborationNamesList);<a name="line.524"></a>
<FONT color="green">525</FONT>        <a name="line.525"></a>
<FONT color="green">526</FONT>        return collaborationNamesList;<a name="line.526"></a>
<FONT color="green">527</FONT>      }<a name="line.527"></a>
<FONT color="green">528</FONT>      <a name="line.528"></a>
<FONT color="green">529</FONT>      /**<a name="line.529"></a>
<FONT color="green">530</FONT>       * Returns the string representation that will be used to generate the javascript array.<a name="line.530"></a>
<FONT color="green">531</FONT>       * <a name="line.531"></a>
<FONT color="green">532</FONT>       * @return The string representation that will be used to generate the javascript array. <a name="line.532"></a>
<FONT color="green">533</FONT>       */<a name="line.533"></a>
<FONT color="green">534</FONT>      public synchronized String getCollaborationNamesList() {<a name="line.534"></a>
<FONT color="green">535</FONT>        List&lt;String&gt; list = getCollaborationNames();<a name="line.535"></a>
<FONT color="green">536</FONT>        String delimiter = "|";<a name="line.536"></a>
<FONT color="green">537</FONT>        StringBuffer names = new StringBuffer();<a name="line.537"></a>
<FONT color="green">538</FONT>        for (String name : list) {<a name="line.538"></a>
<FONT color="green">539</FONT>          names.append(name);<a name="line.539"></a>
<FONT color="green">540</FONT>          names.append(delimiter);<a name="line.540"></a>
<FONT color="green">541</FONT>        }<a name="line.541"></a>
<FONT color="green">542</FONT>    <a name="line.542"></a>
<FONT color="green">543</FONT>        return names.substring(0, (names.length() - 1));<a name="line.543"></a>
<FONT color="green">544</FONT>      }<a name="line.544"></a>
<FONT color="green">545</FONT>     <a name="line.545"></a>
<FONT color="green">546</FONT>      /**<a name="line.546"></a>
<FONT color="green">547</FONT>       * Import the XML researchers data to the Researchers object.<a name="line.547"></a>
<FONT color="green">548</FONT>       * <a name="line.548"></a>
<FONT color="green">549</FONT>       * @param researchersFile A String representation of the researchers XML file.<a name="line.549"></a>
<FONT color="green">550</FONT>       * @return true if the import succeeds, false otherwise.<a name="line.550"></a>
<FONT color="green">551</FONT>       */<a name="line.551"></a>
<FONT color="green">552</FONT>      public synchronized boolean importResearchersXml(String researchersFile) {<a name="line.552"></a>
<FONT color="green">553</FONT>        boolean isImported = true;<a name="line.553"></a>
<FONT color="green">554</FONT>        // try to load in the researchers XML file<a name="line.554"></a>
<FONT color="green">555</FONT>        try {<a name="line.555"></a>
<FONT color="green">556</FONT>          this.researchersJaxbContext = JAXBContext.newInstance("edu.hawaii.myisern.researchers.jaxb");<a name="line.556"></a>
<FONT color="green">557</FONT>          File curFile = new File(researchersFile);<a name="line.557"></a>
<FONT color="green">558</FONT>          // copy the sample file if it does not exist<a name="line.558"></a>
<FONT color="green">559</FONT>          if (!curFile.exists()) {<a name="line.559"></a>
<FONT color="green">560</FONT>            File tempFile = new File(System.getProperty(USER_HOME) + "/.myisern");<a name="line.560"></a>
<FONT color="green">561</FONT>            tempFile.mkdir();<a name="line.561"></a>
<FONT color="green">562</FONT>            File sourceFile = new File(System.getProperty("user.dir") <a name="line.562"></a>
<FONT color="green">563</FONT>                + "/xml/examples/researchers.example.xml");<a name="line.563"></a>
<FONT color="green">564</FONT>            this.copyFile(sourceFile, curFile);<a name="line.564"></a>
<FONT color="green">565</FONT>          }<a name="line.565"></a>
<FONT color="green">566</FONT>          Unmarshaller unmarshaller = this.researchersJaxbContext.createUnmarshaller();<a name="line.566"></a>
<FONT color="green">567</FONT>          System.out.println("Importing researchers data from " + curFile);<a name="line.567"></a>
<FONT color="green">568</FONT>          this.researchers = (Researchers) unmarshaller.unmarshal(curFile);<a name="line.568"></a>
<FONT color="green">569</FONT>        }<a name="line.569"></a>
<FONT color="green">570</FONT>        catch (Exception e) {<a name="line.570"></a>
<FONT color="green">571</FONT>          isImported = false;<a name="line.571"></a>
<FONT color="green">572</FONT>          e.printStackTrace();<a name="line.572"></a>
<FONT color="green">573</FONT>        }<a name="line.573"></a>
<FONT color="green">574</FONT>        // update database tables<a name="line.574"></a>
<FONT color="green">575</FONT>        this.db.writeResearchers(this.researchers);<a name="line.575"></a>
<FONT color="green">576</FONT>        return isImported;<a name="line.576"></a>
<FONT color="green">577</FONT>      }<a name="line.577"></a>
<FONT color="green">578</FONT>      <a name="line.578"></a>
<FONT color="green">579</FONT>      /**<a name="line.579"></a>
<FONT color="green">580</FONT>       * Import the XML organizations data to the Organizations object.<a name="line.580"></a>
<FONT color="green">581</FONT>       * <a name="line.581"></a>
<FONT color="green">582</FONT>       * @param organizationsFile A String representation of the organizations XML file.<a name="line.582"></a>
<FONT color="green">583</FONT>       * @return true if the import succeeds, false otherwise.<a name="line.583"></a>
<FONT color="green">584</FONT>       */<a name="line.584"></a>
<FONT color="green">585</FONT>      public synchronized boolean importOrganizationsXml(String organizationsFile) {<a name="line.585"></a>
<FONT color="green">586</FONT>        boolean isImported = true;<a name="line.586"></a>
<FONT color="green">587</FONT>        // try to load in the Organizations XML file<a name="line.587"></a>
<FONT color="green">588</FONT>        try {<a name="line.588"></a>
<FONT color="green">589</FONT>          this.organizationsJaxbContext = JAXBContext<a name="line.589"></a>
<FONT color="green">590</FONT>              .newInstance("edu.hawaii.myisern.organizations.jaxb");<a name="line.590"></a>
<FONT color="green">591</FONT>          File curFile = new File(organizationsFile);<a name="line.591"></a>
<FONT color="green">592</FONT>          // copy the sample file if it does not exist<a name="line.592"></a>
<FONT color="green">593</FONT>          if (!curFile.exists()) {<a name="line.593"></a>
<FONT color="green">594</FONT>            File tempFile = new File(System.getProperty(USER_HOME) + "/.myisern");<a name="line.594"></a>
<FONT color="green">595</FONT>            tempFile.mkdir();<a name="line.595"></a>
<FONT color="green">596</FONT>            File sourceFile = new File(System.getProperty("user.dir") <a name="line.596"></a>
<FONT color="green">597</FONT>                + "/xml/examples/organizations.example.xml");<a name="line.597"></a>
<FONT color="green">598</FONT>            this.copyFile(sourceFile, curFile);<a name="line.598"></a>
<FONT color="green">599</FONT>          }<a name="line.599"></a>
<FONT color="green">600</FONT>          Unmarshaller unmarshaller = this.organizationsJaxbContext.createUnmarshaller();<a name="line.600"></a>
<FONT color="green">601</FONT>          System.out.println("Importing organizations data from " + curFile);<a name="line.601"></a>
<FONT color="green">602</FONT>          this.organizations = (Organizations) unmarshaller.unmarshal(curFile);<a name="line.602"></a>
<FONT color="green">603</FONT>        }<a name="line.603"></a>
<FONT color="green">604</FONT>        catch (Exception e) {<a name="line.604"></a>
<FONT color="green">605</FONT>          isImported = false;<a name="line.605"></a>
<FONT color="green">606</FONT>          e.printStackTrace();<a name="line.606"></a>
<FONT color="green">607</FONT>        }    <a name="line.607"></a>
<FONT color="green">608</FONT>        // update database tables<a name="line.608"></a>
<FONT color="green">609</FONT>        this.db.writeOrganizations(this.organizations);<a name="line.609"></a>
<FONT color="green">610</FONT>        return isImported;<a name="line.610"></a>
<FONT color="green">611</FONT>      }<a name="line.611"></a>
<FONT color="green">612</FONT>      <a name="line.612"></a>
<FONT color="green">613</FONT>      /**<a name="line.613"></a>
<FONT color="green">614</FONT>       * Import the XML collaborations data to the Collaborations object.<a name="line.614"></a>
<FONT color="green">615</FONT>       * <a name="line.615"></a>
<FONT color="green">616</FONT>       * @param collaborationsFile A String representation of the collaborations XML file.<a name="line.616"></a>
<FONT color="green">617</FONT>       * @return true if the import succeeds, false otherwise.<a name="line.617"></a>
<FONT color="green">618</FONT>       */<a name="line.618"></a>
<FONT color="green">619</FONT>      public synchronized boolean importCollaborationsXml(String collaborationsFile) {<a name="line.619"></a>
<FONT color="green">620</FONT>        boolean isImported = true;<a name="line.620"></a>
<FONT color="green">621</FONT>        // try to load in the Collaborations XML file<a name="line.621"></a>
<FONT color="green">622</FONT>        try {<a name="line.622"></a>
<FONT color="green">623</FONT>          this.collaborationsJaxbContext = JAXBContext<a name="line.623"></a>
<FONT color="green">624</FONT>              .newInstance("edu.hawaii.myisern.collaborations.jaxb");<a name="line.624"></a>
<FONT color="green">625</FONT>          File curFile = new File(collaborationsFile);<a name="line.625"></a>
<FONT color="green">626</FONT>          // copy the sample file if it does not exist<a name="line.626"></a>
<FONT color="green">627</FONT>          if (!curFile.exists()) {<a name="line.627"></a>
<FONT color="green">628</FONT>            File tempFile = new File(System.getProperty(USER_HOME) + "/.myisern");<a name="line.628"></a>
<FONT color="green">629</FONT>            tempFile.mkdir();<a name="line.629"></a>
<FONT color="green">630</FONT>            File sourceFile = new File(System.getProperty("user.dir") <a name="line.630"></a>
<FONT color="green">631</FONT>                + "/xml/examples/collaborations.example.xml");<a name="line.631"></a>
<FONT color="green">632</FONT>            this.copyFile(sourceFile, curFile);<a name="line.632"></a>
<FONT color="green">633</FONT>          }<a name="line.633"></a>
<FONT color="green">634</FONT>          Unmarshaller unmarshaller = this.collaborationsJaxbContext.createUnmarshaller();<a name="line.634"></a>
<FONT color="green">635</FONT>          System.out.println("Importing collaborations data from " + curFile);<a name="line.635"></a>
<FONT color="green">636</FONT>          this.collaborations = (Collaborations) unmarshaller.unmarshal(curFile);<a name="line.636"></a>
<FONT color="green">637</FONT>        }<a name="line.637"></a>
<FONT color="green">638</FONT>        catch (Exception e) {<a name="line.638"></a>
<FONT color="green">639</FONT>          isImported = false;<a name="line.639"></a>
<FONT color="green">640</FONT>          e.printStackTrace();<a name="line.640"></a>
<FONT color="green">641</FONT>        }<a name="line.641"></a>
<FONT color="green">642</FONT>        // update database tables<a name="line.642"></a>
<FONT color="green">643</FONT>        this.db.writeCollaborations(this.collaborations);<a name="line.643"></a>
<FONT color="green">644</FONT>        return isImported;<a name="line.644"></a>
<FONT color="green">645</FONT>      }<a name="line.645"></a>
<FONT color="green">646</FONT>        <a name="line.646"></a>
<FONT color="green">647</FONT>      /**<a name="line.647"></a>
<FONT color="green">648</FONT>       * Export all the data by writing to the XML files.<a name="line.648"></a>
<FONT color="green">649</FONT>       * <a name="line.649"></a>
<FONT color="green">650</FONT>       * @param researchersFile A String representation of the researchers XML file.<a name="line.650"></a>
<FONT color="green">651</FONT>       * @param organizationsFile A String representation of the organizations XML file.<a name="line.651"></a>
<FONT color="green">652</FONT>       * @param collaborationsFile A String representation of the collaborations XML file.<a name="line.652"></a>
<FONT color="green">653</FONT>       * @return true if the export succeeds, false otherwise.<a name="line.653"></a>
<FONT color="green">654</FONT>       */  <a name="line.654"></a>
<FONT color="green">655</FONT>      public synchronized boolean exportXml(String researchersFile,<a name="line.655"></a>
<FONT color="green">656</FONT>          String organizationsFile, String collaborationsFile) {<a name="line.656"></a>
<FONT color="green">657</FONT>        boolean isExported = true;<a name="line.657"></a>
<FONT color="green">658</FONT>        // save all changes for researchers<a name="line.658"></a>
<FONT color="green">659</FONT>        try {<a name="line.659"></a>
<FONT color="green">660</FONT>          JAXBContext researchersJaxbContext = JAXBContext<a name="line.660"></a>
<FONT color="green">661</FONT>              .newInstance("edu.hawaii.myisern.researchers.jaxb");<a name="line.661"></a>
<FONT color="green">662</FONT>          Marshaller marshaller = researchersJaxbContext.createMarshaller();<a name="line.662"></a>
<FONT color="green">663</FONT>          // set the marshaller to do formatted output to the XML file<a name="line.663"></a>
<FONT color="green">664</FONT>          marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);<a name="line.664"></a>
<FONT color="green">665</FONT>          // writes the new XML<a name="line.665"></a>
<FONT color="green">666</FONT>          OutputStream os = new FileOutputStream(researchersFile);<a name="line.666"></a>
<FONT color="green">667</FONT>          marshaller.marshal(this.researchers, os);<a name="line.667"></a>
<FONT color="green">668</FONT>          System.out.println("Exporting researchers data to " + researchersFile);<a name="line.668"></a>
<FONT color="green">669</FONT>          os.close();<a name="line.669"></a>
<FONT color="green">670</FONT>        }<a name="line.670"></a>
<FONT color="green">671</FONT>        catch (Exception e) {<a name="line.671"></a>
<FONT color="green">672</FONT>          isExported = false;<a name="line.672"></a>
<FONT color="green">673</FONT>          e.printStackTrace();<a name="line.673"></a>
<FONT color="green">674</FONT>        }<a name="line.674"></a>
<FONT color="green">675</FONT>        try {<a name="line.675"></a>
<FONT color="green">676</FONT>          // save all changes for organizations<a name="line.676"></a>
<FONT color="green">677</FONT>          JAXBContext organizationsJaxbContext = JAXBContext<a name="line.677"></a>
<FONT color="green">678</FONT>              .newInstance("edu.hawaii.myisern.organizations.jaxb");<a name="line.678"></a>
<FONT color="green">679</FONT>          Marshaller marshaller = organizationsJaxbContext.createMarshaller();<a name="line.679"></a>
<FONT color="green">680</FONT>          // set the marshaller to do formatted output to the XML file<a name="line.680"></a>
<FONT color="green">681</FONT>          marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);<a name="line.681"></a>
<FONT color="green">682</FONT>          // writes the new XML<a name="line.682"></a>
<FONT color="green">683</FONT>          OutputStream os = new FileOutputStream(organizationsFile);<a name="line.683"></a>
<FONT color="green">684</FONT>          marshaller.marshal(this.organizations, os);<a name="line.684"></a>
<FONT color="green">685</FONT>          System.out.println("Exporting organizations data to " + organizationsFile);<a name="line.685"></a>
<FONT color="green">686</FONT>          os.close();<a name="line.686"></a>
<FONT color="green">687</FONT>        }<a name="line.687"></a>
<FONT color="green">688</FONT>        catch (Exception e) {<a name="line.688"></a>
<FONT color="green">689</FONT>          isExported = false;<a name="line.689"></a>
<FONT color="green">690</FONT>          e.printStackTrace();<a name="line.690"></a>
<FONT color="green">691</FONT>        }<a name="line.691"></a>
<FONT color="green">692</FONT>        try {<a name="line.692"></a>
<FONT color="green">693</FONT>          // save all changes for collaborations<a name="line.693"></a>
<FONT color="green">694</FONT>          JAXBContext collaborationsJaxbContext = JAXBContext<a name="line.694"></a>
<FONT color="green">695</FONT>              .newInstance("edu.hawaii.myisern.collaborations.jaxb");<a name="line.695"></a>
<FONT color="green">696</FONT>          Marshaller marshaller = collaborationsJaxbContext.createMarshaller();<a name="line.696"></a>
<FONT color="green">697</FONT>          // set the marshaller to do formatted output to the XML file<a name="line.697"></a>
<FONT color="green">698</FONT>          marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);<a name="line.698"></a>
<FONT color="green">699</FONT>          // writes the new XML<a name="line.699"></a>
<FONT color="green">700</FONT>          OutputStream os = new FileOutputStream(collaborationsFile);<a name="line.700"></a>
<FONT color="green">701</FONT>          marshaller.marshal(this.collaborations, os);<a name="line.701"></a>
<FONT color="green">702</FONT>          System.out.println("Exporting collaborations data to " + collaborationsFile);<a name="line.702"></a>
<FONT color="green">703</FONT>          os.close();<a name="line.703"></a>
<FONT color="green">704</FONT>        }<a name="line.704"></a>
<FONT color="green">705</FONT>        catch (Exception e) {<a name="line.705"></a>
<FONT color="green">706</FONT>          isExported = false;<a name="line.706"></a>
<FONT color="green">707</FONT>          e.printStackTrace();<a name="line.707"></a>
<FONT color="green">708</FONT>        }<a name="line.708"></a>
<FONT color="green">709</FONT>        return isExported;<a name="line.709"></a>
<FONT color="green">710</FONT>      }<a name="line.710"></a>
<FONT color="green">711</FONT>    <a name="line.711"></a>
<FONT color="green">712</FONT>      /**<a name="line.712"></a>
<FONT color="green">713</FONT>       * Helper method to copy the sample XML files.<a name="line.713"></a>
<FONT color="green">714</FONT>       * This method is inspired from http://www.rgagnon.com/javadetails/java-0064.html<a name="line.714"></a>
<FONT color="green">715</FONT>       * <a name="line.715"></a>
<FONT color="green">716</FONT>       * @param in Source file.<a name="line.716"></a>
<FONT color="green">717</FONT>       * @param out Destination file.<a name="line.717"></a>
<FONT color="green">718</FONT>       * @throws Exception If error occurs.<a name="line.718"></a>
<FONT color="green">719</FONT>       */<a name="line.719"></a>
<FONT color="green">720</FONT>      protected synchronized void copyFile(File in, File out) throws Exception {<a name="line.720"></a>
<FONT color="green">721</FONT>        FileChannel inChannel = null;<a name="line.721"></a>
<FONT color="green">722</FONT>        FileChannel outChannel = null;<a name="line.722"></a>
<FONT color="green">723</FONT>        try {<a name="line.723"></a>
<FONT color="green">724</FONT>          inChannel = new FileInputStream(in).getChannel();<a name="line.724"></a>
<FONT color="green">725</FONT>          outChannel = new FileOutputStream(out).getChannel(); <a name="line.725"></a>
<FONT color="green">726</FONT>          inChannel.transferTo(0, inChannel.size(), outChannel);<a name="line.726"></a>
<FONT color="green">727</FONT>          System.out.println("Copying from " + in + " to " + out);<a name="line.727"></a>
<FONT color="green">728</FONT>        } <a name="line.728"></a>
<FONT color="green">729</FONT>        catch (Exception e) {<a name="line.729"></a>
<FONT color="green">730</FONT>          e.printStackTrace();<a name="line.730"></a>
<FONT color="green">731</FONT>        }<a name="line.731"></a>
<FONT color="green">732</FONT>        finally {<a name="line.732"></a>
<FONT color="green">733</FONT>          if (inChannel != null) { <a name="line.733"></a>
<FONT color="green">734</FONT>            inChannel.close();<a name="line.734"></a>
<FONT color="green">735</FONT>          }<a name="line.735"></a>
<FONT color="green">736</FONT>          if (outChannel != null) { <a name="line.736"></a>
<FONT color="green">737</FONT>            outChannel.close();<a name="line.737"></a>
<FONT color="green">738</FONT>          }<a name="line.738"></a>
<FONT color="green">739</FONT>        }<a name="line.739"></a>
<FONT color="green">740</FONT>      }<a name="line.740"></a>
<FONT color="green">741</FONT>    }<a name="line.741"></a>




























































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